Both Fred and Illyria were crying.
The line where Fred ends and Illyria begins became very hazy, as even Fred's prefrences about the world came out of Illyria, and she was completely natural and accepting of it. (In either Power Play or Not Fade Away, Illyria tells Gunn that she doesn't find him unpleasent to her eyes.)
Beyond that, there's a lot of arguments that say that Illyria isn't still "Illyria". The Mutari Generator, sure. She even says that she is her power, implying anything less would be a different being.
Looking at text in the show, though, it's deeper than that. Much.
In "A Hole In The World", near the end of the episode, Fred is on her bed and begins hallucinating, points to Wesley and says "I'm with him!" After she calms down she takes Wesley's hand, places it on her heart, and says "He's with me." It's very clear to me that the demon god Illyria became tied to Wesley before she even destroyed Fred's soul by ressurecting, and becoming bound to Fred ("I could change it if I cared to", is what she said, I believe, in refrence to that subject).
Which, also, points to the notion that Fred and Illyria are one being. If you placed, say, a stack of paper of top of a pizza, inside of a box, then cooked it, would the ash not taint and be a factor in all the changes that would then occur to everything having to do with the pizza?
The paper would be Fred's soul, the pizza is capacity of life, the box is the physical shell, and the oven is Illyria. Even though Fred's soul may have been burnt, as paper would be, all that Illyria was changed the moment she clawed her way into Fred's body, becoming saturated with not just humanity- but the humanity of Winifred Burkle.
I could continue on, but, in summation, I believe the continued existance of both Fred and Illyria makes them reliant on one another, and the tears were from them both.